Mar 13, 2015

Strategies for calculating blockwise likelihoods under the coalescent

BioRxiv : the Preprint Server for Biology
Konrad LohseNick H Barton


The inference of demographic history from genome data is hindered by a lack of efficient computational approaches. In particular, it has proven difficult to exploit the information contained in the distribution of genealogies across the genome. We have previously shown that the generating function (GF) of genealogies can be used to analytically compute likelihoods of demographic models from configurations of mutations in short sequence blocks. Although the GF has a simple, recursive form ([Lohse et al. , 2011][1]), the size of such likelihood computations explodes quickly with the number of individuals and applications of this framework have so far been limited to small samples (pairs and triplets). Here we investigate several strategies for exploiting the inherent symmetries of the coalescent and approximating the models that include reversible events. In particular, we show that the GF of genealogies can be decomposed into a set of equivalence classes which allows likelihood calculations from non-trivial samples. As an example, we implement block-wise likelihood calculations for a model of isolation with migration (IM) and two diploid samples without phase and outgroup information and compare the power of this approach to tha...Continue Reading

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Mentioned in this Paper

Isolation Aspects
Genetic Pedigree
Triplet, Centriole
Diploid Cell
Automate (invertebrate)

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